qscores: Examples of qscore objects (quality scores) to apply to CGH...

In MANOR: CGH Micro-Array NORmalization

Description

This data set provides qscore objects that can be applied to normalized arrayCGH objects in order to evaluate data quality after normalization.

Usage

data(qscores)

Format

The following qscore objects are provided:

	clone.qscore	number of clones
	pct.clone.qscore	percentage of clones
	pct.spot.qscore	percentage of spots
	pct.spot.before.qscore	percentage of spots before normalization
	pct.replicate.qscore	average percentage of replicates
	smoothness.qscore	signal smoothness
	var.replicate.qscore
	dyn.x.qscore	signal dynamics on X chromosome
	dyn.y.qscore	signal dynamics on Y chromosome

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Pierre Neuvial, [e-mail].

Source

Institut Curie, [e-mail].

See Also

spatial, qscore.summary.arrayCGH, qscore

Examples

data(qscores)
data(spatial)

## define a list of qscores
qscore.list <- list(clone=clone.qscore, pct.clone=pct.clone.qscore,
pct.spot=pct.spot.qscore, pct.replicate=pct.replicate.qscore,
smoothness=smoothness.qscore, dyn.x=dyn.x.qscore, dyn.y=dyn.y.qscore,
var.replicate=var.replicate.qscore)

## compute quality scores for a couple of normalized arrays
gradient.norm$quality <- qscore.summary.arrayCGH(gradient.norm,
qscore.list)
print(gradient.norm$quality[, 2:3])

qscore.list$dyn.x$args$test <- 23
qscore.list$dyn.y$args$test <- 24
edge.norm$quality <- qscore.summary.arrayCGH(edge.norm, qscore.list)
print(edge.norm$quality[, 2:3])

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.